Reciprocal Grids: A Hierarchical Algorithm for Computing Solution X-ray Scattering Curves from Supramolecular Complexes at High Resolution

Avi Ginsburg, Tal Ben-Nun, Roi Asor, Asaf Shemesh, Israel Ringel, Uri Raviv*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

25 Scopus citations

Abstract

In many biochemical processes large biomolecular assemblies play important roles. X-ray scattering is a label-free bulk method that can probe the structure of large self-assembled complexes in solution. As we demonstrate in this paper, solution X-ray scattering can measure complex supramolecular assemblies at high sensitivity and resolution. At high resolution, however, data analysis of larger complexes is computationally demanding. We present an efficient method to compute the scattering curves from complex structures over a wide range of scattering angles. In our computational method, structures are defined as hierarchical trees in which repeating subunits are docked into their assembly symmetries, describing the manner subunits repeat in the structure (in other words, the locations and orientations of the repeating subunits). The amplitude of the assembly is calculated by computing the amplitudes of the basic subunits on 3D reciprocal-space grids, moving up in the hierarchy, calculating the grids of larger structures, and repeating this process for all the leaves and nodes of the tree. For very large structures, we developed a hybrid method that sums grids of smaller subunits in order to avoid numerical artifacts. We developed protocols for obtaining high-resolution solution X-ray scattering data from taxol-free microtubules at a wide range of scattering angles. We then validated our method by adequately modeling these high-resolution data. The higher speed and accuracy of our method, over existing methods, is demonstrated for smaller structures: short microtubule and tobacco mosaic virus. Our algorithm may be integrated into various structure prediction computational tools, simulations, and theoretical models, and provide means for testing their predicted structural model, by calculating the expected X-ray scattering curve and comparing with experimental data.

Original languageAmerican English
Pages (from-to)1518-1527
Number of pages10
JournalJournal of Chemical Information and Modeling
Volume56
Issue number8
DOIs
StatePublished - 22 Aug 2016

Bibliographical note

Publisher Copyright:
© 2016 American Chemical Society.

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